Bash script BLAST
1. Take all the proteins annotated in the chromosome 1 of Arabidopsis thaliana (TAIR proteins FASTA). Hint1: The ids of the proteins in chromosome 1 start with AT1. Hint2: You can use EMBOSS's seqret for this.
2. Take the first 40 aminoacids of each protein from step 1. Hint 3: you can use EMBOSS's extractseq
3. Blast each protein against the file TAIR cDNA fasta, keeping the first 2 hits Hint 4: Perhaps prior to BLASTing you could use EMBOSS's seqretsplit, and then use a for loop in your script. . .